rs772158281
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7
The NM_004370.6(COL12A1):c.177G>A(p.Val59=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000481 in 1,456,324 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000048 ( 0 hom. )
Consequence
COL12A1
NM_004370.6 synonymous
NM_004370.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.452
Genes affected
COL12A1 (HGNC:2188): (collagen type XII alpha 1 chain) This gene encodes the alpha chain of type XII collagen, a member of the FACIT (fibril-associated collagens with interrupted triple helices) collagen family. Type XII collagen is a homotrimer found in association with type I collagen, an association that is thought to modify the interactions between collagen I fibrils and the surrounding matrix. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.35).
BP6
Variant 6-75194844-C-T is Benign according to our data. Variant chr6-75194844-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 475845.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.452 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL12A1 | NM_004370.6 | c.177G>A | p.Val59= | synonymous_variant | 3/66 | ENST00000322507.13 | NP_004361.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL12A1 | ENST00000322507.13 | c.177G>A | p.Val59= | synonymous_variant | 3/66 | 1 | NM_004370.6 | ENSP00000325146 | P4 | |
COL12A1 | ENST00000345356.10 | c.73+7876G>A | intron_variant | 1 | ENSP00000305147 | |||||
COL12A1 | ENST00000483888.6 | c.177G>A | p.Val59= | synonymous_variant | 3/65 | 5 | ENSP00000421216 | A1 | ||
COL12A1 | ENST00000416123.6 | c.177G>A | p.Val59= | synonymous_variant | 2/63 | 5 | ENSP00000412864 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
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33
GnomAD3 exomes AF: 0.00000809 AC: 2AN: 247088Hom.: 0 AF XY: 0.00000746 AC XY: 1AN XY: 134070
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GnomAD4 exome AF: 0.00000481 AC: 7AN: 1456324Hom.: 0 Cov.: 29 AF XY: 0.00000414 AC XY: 3AN XY: 724554
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GnomAD4 genome Cov.: 33
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33
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Bethlem myopathy 2;C4225314:Ullrich congenital muscular dystrophy 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 09, 2020 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at